Diversity of Reptiles in the ACT

library(here)
library(galah)
library(skimr)
library(dplyr)
library(lubridate)
library(stringr)
library(ggplot2)
library(leaflet)
library(leaflet.extras)
library(reactable)
library(scico)

reptilia <- readRDS(here("data", "reptilia"))

reptilia_tidy <- reptilia %>% 
  filter(cl22 == "Australian Capital Territory") %>% 
  rename(state = cl22, 
         forestType = cl10902) %>% 
  mutate(forestType = na_if(forestType, ""),
         basisOfRecord = tolower(basisOfRecord),
         basisOfRecord = str_replace(basisOfRecord, "_", " "),
         eventDate = as_datetime(eventDate, tz = "Australia/Sydney", format = NULL),
         eventDate = as_date(eventDate, tz = NULL),
         month = month(eventDate))

skim(reptilia_tidy)

Data summary

Name	reptilia_tidy
Number of rows	10145
Number of columns	12
_______________________
Column type frequency:
character	8
Date	1
numeric	3
________________________
Group variables	None

Variable type: character

skim_variable	n_missing	complete_rate	min	max	empty	n_unique	whitespace
scientificName	0	1	4	33	0	102	0
genus	0	1	0	16	106	52	0
family	0	1	0	15	38	12	0
order	0	1	0	10	4	3	0
dataResourceName	0	1	9	87	0	23	0
basisOfRecord	0	1	7	18	0	5	0
state	0	1	28	28	0	1	0
forestType	17	1	6	31	0	10	0

Variable type: Date

skim_variable	n_missing	complete_rate	min	max	median	n_unique
eventDate	5206	0.49	1954-01-22	2021-11-25	2012-10-08	1783

Variable type: numeric

skim_variable	n_missing	complete_rate	mean	sd	p0	p25	p50	p75	p100	hist
decimalLatitude	0	1.00	-35.34	0.15	-35.91	-35.40	-35.3	-35.24	-35.12	▁▁▃▇▇
decimalLongitude	0	1.00	149.11	0.30	148.76	148.99	149.1	149.15	150.77	▇▂▁▁▁
month	5206	0.49	7.92	3.92	1.00	3.00	10.0	11.00	12.00	▃▁▁▂▇

# remove cols not of interest in a table
reptilia_subset <- reptilia_tidy %>% 
  select(eventDate:basisOfRecord, forestType)

reactable(
  reptilia_subset,
  columns = list(
    eventDate = colDef(name = "Date"),
    scientificName = colDef(name = "Species"),
    genus = colDef(name = "Genus"),
    family = colDef(name = "Family"),
    order = colDef(name = "Order"),
    dataResourceName = colDef(name = "Source"),
    basisOfRecord = colDef(name = "Record type"),
    forestType = colDef(name = "Forest type")
  ),
  showSortable = TRUE,
  filterable = TRUE,
  searchable = TRUE,
  showPageInfo = FALSE,
  striped = TRUE
)

Citation

ALA occurrence download https://doi.org/10.26197/ala.1999d964-1ccc-44f5-8cba-ed7ec33b1e41. Accessed from R with galah 1.3.1 (https://github.com/AtlasOfLivingAustralia/galah/) on 2021-12-04.